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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 08:56:45 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 08:56:45 +0200
commitec1487f0f2cef32d44b0c6ce94a6f1b4f65a79d3 (patch)
tree10820a2fa5ae6b51115c2d2f40e40bcc8f0b8d5e /inst/web/plot.mkinfit.html
parent6b7c2049d4feb9dd76dd532830adba23b8a5007f (diff)
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-<!DOCTYPE html>
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-<title>plot.mkinfit. mkin 0.9.44.9000</title>
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- Johannes Ranke
-">
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- <a class="brand" href="#">mkin 0.9.44.9000</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>
- Plot the observed data and the fitted model of an mkinfit object
-</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><div>"plot"(x, fit&nbsp;=&nbsp;x, obs_vars&nbsp;=&nbsp;names(fit$mkinmod$map), xlab&nbsp;=&nbsp;"Time", ylab&nbsp;=&nbsp;"Observed", xlim&nbsp;=&nbsp;range(fit$data$time), ylim&nbsp;=&nbsp;"default", col_obs&nbsp;=&nbsp;1:length(obs_vars), pch_obs&nbsp;=&nbsp;col_obs, lty_obs&nbsp;=&nbsp;rep(1, length(obs_vars)), add&nbsp;=&nbsp;FALSE, legend&nbsp;=&nbsp;!add, show_residuals&nbsp;=&nbsp;FALSE, maxabs&nbsp;=&nbsp;"auto", sep_obs&nbsp;=&nbsp;FALSE, rel.height.middle&nbsp;=&nbsp;0.9, lpos&nbsp;=&nbsp;"topright", inset&nbsp;=&nbsp;c(0.05, 0.05), show_errmin&nbsp;=&nbsp;FALSE, errmin_digits&nbsp;=&nbsp;3, ...)
-plot_sep(fit, sep_obs&nbsp;=&nbsp;TRUE, show_residuals&nbsp;=&nbsp;TRUE, show_errmin&nbsp;=&nbsp;TRUE, ...)</div></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>x</dt>
- <dd>
- Alias for fit introduced for compatibility with the generic S3 method.
- </dd>
- <dt>fit</dt>
- <dd>
- An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
- </dd>
- <dt>obs_vars</dt>
- <dd>
- A character vector of names of the observed variables for which the
- data and the model should be plotted. Defauls to all observed variables
- in the model.
- </dd>
- <dt>xlab</dt>
- <dd>
- Label for the x axis.
- </dd>
- <dt>ylab</dt>
- <dd>
- Label for the y axis.
- </dd>
- <dt>xlim</dt>
- <dd>
- Plot range in x direction.
- </dd>
- <dt>ylim</dt>
- <dd>
- Plot range in y direction.
- </dd>
- <dt>col_obs</dt>
- <dd>
- Colors used for plotting the observed data and the corresponding model prediction lines.
- </dd>
- <dt>pch_obs</dt>
- <dd>
- Symbols to be used for plotting the data.
- </dd>
- <dt>lty_obs</dt>
- <dd>
- Line types to be used for the model predictions.
- </dd>
- <dt>add</dt>
- <dd>
- Should the plot be added to an existing plot?
- </dd>
- <dt>legend</dt>
- <dd>
- Should a legend be added to the plot?
- </dd>
- <dt>show_residuals</dt>
- <dd>
- Should residuals be shown? If only one plot of the fits is shown, the
- residual plot is in the lower third of the plot? Otherwise, i.e. if
- "sep_obs" is given, the residual plots will be located to the right of
- the plots of the fitted curves.
- </dd>
- <dt>maxabs</dt>
- <dd>
- Maximum absolute value of the residuals. This is used for the scaling of
- the y axis and defaults to "auto".
- </dd>
- <dt>sep_obs</dt>
- <dd>
- Should the observed variables be shown in separate subplots? If yes, residual plots
- requested by "show_residuals" will be shown next to, not below the plot of the fits.
- </dd>
- <dt>rel.height.middle</dt>
- <dd>
- The relative height of the middle plot, if more than two rows of plots are shown.
- </dd>
- <dt>lpos</dt>
- <dd>
- Position(s) of the legend(s). Passed to <code><a href='http://www.inside-r.org/r-doc/graphics/legend'>legend</a></code> as the first argument.
- If not length one, this should be of the same length as the obs_var argument.
- </dd>
- <dt>inset</dt>
- <dd>
- Passed to <code><a href='http://www.inside-r.org/r-doc/graphics/legend'>legend</a></code> if applicable.
- </dd>
- <dt>show_errmin</dt>
- <dd>
- Should the FOCUS chi2 error value be shown in the upper margin of the plot?
- </dd>
- <dt>errmin_digits</dt>
- <dd>
- The number of significant digits for rounding the FOCUS chi2 error percentage.
- </dd>
- <dt>...</dt>
- <dd>
- Further arguments passed to <code><a href='http://www.inside-r.org/r-doc/graphics/plot'>plot</a></code>.
- </dd>
- </dl>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Solves the differential equations with the optimised and fixed parameters
- from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots
- the observed data together with the solution of the fitted model.</p>
-
- </div>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
- The function is called for its side effect.
-</dl></p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'># One parent compound, one metabolite, both single first order, path from
-# parent to sink included, use Levenberg-Marquardt for speed
-SFO_SFO &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;, full = &quot;Parent&quot;),
- m1 = mkinsub(&quot;SFO&quot;, full = &quot;Metabolite M1&quot; ))
-</div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'>fit &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = &quot;Marq&quot;)
-plot(fit)
-</div>
-<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p>
-<div class='input'>plot(fit, show_residuals = TRUE)
-</div>
-<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p>
-<div class='input'>
-# Show the observed variables separately
-plot(fit, sep_obs = TRUE, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;))
-</div>
-<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p>
-<div class='input'>
-# Show the observed variables separately, with residuals
-plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;),
- show_errmin = TRUE)
-</div>
-<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p>
-<div class='input'>
-# The same can be obtained with less typing, using the convenience function plot_sep
-plot_sep(fit, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;))
-</div></pre>
- </div>
- <div class="span4">
- <!-- <ul>
- <li>plot.mkinfit</li><li>plot_sep</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
- <h2>Author</h2>
-
- Johannes Ranke
-
-
- </div>
-</div>
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